Using Analyze

CEREBELLUM SEGMENTATIONAND VOLUME MEASUREMENT

Table of Contents

2CEREBELLUM SEGMENTATION AND VOLUME MEASUREMENT

1. Introduction page 3

2. Segmentation of the Cerebellum page 4

3. Measurement of Cerebellar Volume page 8

4. References page 10

3CEREBELLUM SEGMENTATION AND VOLUME MEASUREMENT

Introduction

The cerebellum is an active area of brain research. It has long been associated with motor coordination, but more recently it has been

shown to play a role in cognition and learning as well1. Its structure, and thus its volume, has been shown to exhibit plasticity based on an

individual’s experiences and environmental stressors2.

Cerebellar volume has been found to decrease with age, driven by loss of white matter3. Smaller cerebellar volume was associated with

diabetes, low total cholesterol, high fasting glucose, low HDL cholesterol3, major depressive disorder4, and schizophrenia,5 or schizophrenia

combined with alcoholism6. The cerebella of children from multiplex alcohol dependence families7 appear to have increased volume

compared to controls, which may indicate a lower functional efficiency of this structure.

Interconnectivity between the cerebellum and the cerebrum has been demonstrated in different ways. Constrained spherical deconvolution

analysis was used to show a pathway linking the cerebellum and limbic structures8. Supratentorial lacunar infarcts and white matter lesions in

the cerebrum have been found to be associated with decreased cerebellar volume3.

The cerebellum has a similar intensity to the rest of brain in MRI images. One way of separating it from other brain structures is by using

three-dimensional walls to define boundaries, then using the object extractor algorithm to extract the cerebellum.

This guide will describe in detail how to segment the cerebellum from MRI brain data and measure its volume in Analyze.

4CEREBELLUM SEGMENTATION AND VOLUME MEASUREMENT

Segmentation of the Cerebellum

Use the Load module (File > Load) to load the example MRI brain data set

MRI_EGV_Brain.avw from $:\BIR\images\TutorialData, where $ is the drive

where you have installed the TutorialData folder. This folder can also be

downloaded from http://analyzedirect.com/data/

Select the data set in the Analyze workspace and open the Volume Edit

module (Segment > Volume Edit).

If detailed structures are hard to see, as in this data set, adjust the range

of grayscale intensities displayed from the Intensity Images window (View > Intensities) by moving the sliders. In the case of the example data, the

maximum value should be decreased until the brain structures become

visible, around 80-100.

Select the Walls tab and check the “Define walls to limit semi-automated operations” checkbox. Choose the Draw Wall radio button

and set the Wall Type to Spline.

5CEREBELLUM SEGMENTATION AND VOLUME MEASUREMENT

Navigate through the sagittal slices to find the first slice that includes tissue belonging to the cerebellum. In the example data set, this is

slice 68. Draw a wall separating the cerebellum from the cerebrum on this slice. To draw a wall using the spline tool, left-click to set spline

points which will connect into a smooth line. Double click when defining the last spline point to set the spline. The spline points can be

adjusted by clicking and dragging them with the middle mouse button. Once you are happy with the spline, click the Apply button or hit the

A key to apply the spline.

Tip: Draw walls that are not completed closed shapes. If the walls are closed, sometimes the interpolation will not stay around the shape of the

cerebellum. Instead, draw an open U or C shape, letting natural intensity boundaries in the image define the open part of the wall.

Navigate through the sagittal images. A dotted line will indicate the position of the wall as you move through the slices. Once the

cerebellum is no longer well defined by the wall, redefine the wall on that slice. The wall will be interpolated between all slices on which it is

defined. When finished, scroll through the slices to ensure that the cerebellum is well defined by the wall.

6CEREBELLUM SEGMENTATION AND VOLUME MEASUREMENT

Now that the cerebellum boundary is defined in three dimensions by

the wall, we will use the object extractor algorithm to segment the

cerebellum. Select the Semi-Automatic tab and choose the Object Extractor radio button. Click in the cerebellum on a sagittal slice to

set a seed point.

Select a threshold range that defines the brain tissue. For the

example data set, the threshold range 30-69 works well.

Click the Extract Object button to extract the cerebellum.

7CEREBELLUM SEGMENTATION AND VOLUME MEASUREMENT

Note: If you wish to segment the cerebrum, lock the cerebellum object by clicking

the padlock icon to the left of Object_2. Click the Add Object button to add a new

object. Navigate through the transverse slices until the brain is spatially connected.

Set a seed point in the brain on the spatially connected transverse slice. Click the

Extract Object button to segment the cerebrum.

Save the object map to disk (File > Save Object Map) and close the Volume

Edit module.

8CEREBELLUM SEGMENTATION AND VOLUME MEASUREMENT

Measurement of Cerebellar Volume

Select the data set in the Analyze workspace and

open the Region of Interest module (Measure > Region of Interest). Load the object map

created in the segmentation step (File > Load Object Map).

To open the measurements tool, click Generate > Sample Options.

In the Sample Options window, set the following

parameters:

• Sample Type to Object(s)

• Select the Cerebellum Object

• Summing to On• Sample to All Slices• Sequence Display to Off• Log Stats to On• Specify number of decimal places

Click on the Configure Log Stats button. The

ROI Stats window will open, showing the measurements that can be generated. Uncheck the

Area measurement.

9CEREBELLUM SEGMENTATION AND VOLUME MEASUREMENT

In the Sample Options window, click the Sample Images button to measure the volume of the cerebellum. The ROI Stat Log window will

open and show the measured values. Save this data as a .stats file by clicking the Save button or right-clicking in the window and clicking

Save Log or Save Log As.

10

References

CEREBELLUM SEGMENTATION AND VOLUME MEASUREMENT

5. Bottmer, C. et al. Reduced cerebellar volume and

neurological soft signs in first-episode schizophrenia.

Psychiatry Res. 140, 239-50 (2005).

6. Sullivan, E. V. et al. Contribution of Alcohol Abuse to

Cerebellar Volume Deficits in Men With Schizophrenia. Arch.

Gen. Psychiatry 57, 894 (2000).

7. Hill, S. Y. et al. Cerebellar Volume in Offspring From

Multiplex Alcohol Dependence Families. Biol. Psychiatry 61,

41–47 (2007).

8. Arrigo, A. et al. Constrained Spherical Deconvolution analysis

of the limbic network in human, with emphasis on a direct

cerebello-limbic pathway Citation: Constrained Spherical

Deconvolution analysis of the limbic network in hu. (2014).

doi:10.3389/fnhum.2014.00987

1. Courchesne, E. & Allen, G. Prediction and Preparation,

Fundamental Functions of the Cerebellum. Learn. Mem. 4,

1-35 (1997).

2. Bauer, P. M., Hanson, J. L., Pierson, R. K., Davidson, R. J. &

Pollak, S. D. Cerebellar Volume and Cognitive Functioning in

Children Who Experienced Early Deprivation. Biol. Psychiatry

66, 1100-1106 (2009).

3. Hoogendam, Y. Y. et al. Determinants of cerebellar and

cerebral volume in the general elderly population. Neurobiol.

Aging 33, 2774-81 (2012).

4. Escalona, P. R. et al. Reduction of Cerebellar Volume in

Major Depression: A Controlled MRI Study. Depression 1,

156-158 (1993).

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